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Monarch Documentation

The Monarch Initiative and our collaborators develop a wide range of tools and ontologies to tackle global challenges such as Rare Disease. Here we document the software and data infrastructure across the entire Monarch ecosystem. If you would like any specific documentation to be added please use our Monarch-wide issue tracker.

Standards documentation

Repository Description Tracker
Phenopackets An ISO-endorsed open standard for sharing disease and phenotype information. Issue Tracker
Simple Standard for Ontology Mappings (SSSOM) A simple metadata standard for describing semantic mappings. Issue Tracker
Human Phenotype Ontology Provides a standardized vocabulary of phenotypic abnormalities in human disease. Issue Tracker
obographs The obographs ontology format aims and providing a simple graph-oriented JSON format for ontologies. Issue Tracker
Mondo Disease Ontology Aims to harmonize disease definitions across the world. Issue Tracker
Genotype Ontology An ontology that represents the levels of genetic variation specified in genotypes. Issue Tracker
Scientific Evidence and Provenance Information Ontology An ontology that supports the description of evidence and provenance information for scientific claims. Issue Tracker
Vertebrate Breed Ontology An ontology created to serve as a single computable resource for vertebrate breed names. Issue Tracker
The Unified Phenotype Ontology (uPheno) Aims to unify the annotation of phenotypes across species. Issue Tracker
Medical Action Ontology Issue Tracker
Ontology of Biological Attributes Issue Tracker
Uberon Anatomy Ontology An integrated cross-species anatomy ontology. Issue Tracker
Environmental Exposure Ontology Issue Tracker
Dead simple owl design pattern (DOS-DP) exchange format Issue Tracker
Knowledge Graph Change Language Issue Tracker
Babelon - A simple standard for managing ontology translations and language profiles Issue Tracker

Tools documentation

Repository Description Tracker
Exomiser A tool for finding potential disease-causing variants in whole-exome or whole-genome sequencing data. Issue Tracker
Monarch Knowledge Graph & Services Integrates gene, disease, and phenotype data across species. Issue Tracker
Monarch App A web application for exploring the Monarch Knowledge Graph. Issue Tracker
Monarch API The Monarch API is used to access information from the Monarch Knowledge Graph programmatically. Issue Tracker
Ontology Development Kit (ODK) A toolkit and workflow system for managing the ontology life-cycle. Issue Tracker
Ontology Access Kit (OAK) A python toolkit for accessing and visualising ontologies. Issue Tracker
SSSOM Toolkit A python toolkit for processing SSSOM mapping files. Issue Tracker
LIkelihood Ratio Interpretation of Clinical AbnormaLities (LIRICAL) LIkelihood Ratio Interpretation of Clinical AbnormaLities performs phenotype-driven prioritization of candidate diseases and genes in the setting of genomic diagnostics. Issue Tracker
PhEval PhEval is a Python package for evaluating phenotype-powered variant prioritisation systems such as Exomiser. Issue Tracker
obographviz Issue Tracker
robot Issue Tracker
OntoGPT OntoGPT is a Python package for extracting structured information from text with large language models (LLMs), instruction prompts, and ontology-based grounding. Issue Tracker
CurateGPT AI Assisted Ontology Curation. Issue Tracker
Monarch Python Toolkit Issue Tracker
Babelon Toolkit Issue Tracker
Fenominal Issue Tracker
Koza Issue Tracker
LinkML The Linked Data Modeling Language (LinkML) is a flexible modeling language that allows you to author schemas (models) in YAML that describe the structure of your data. Issue Tracker
Monarch Ingest The Monarch Ingest pulls in data from a wide variety of biomedical data sources and generates Biolink-compliant KGX files that are used to build the Monarch KG. Issue Tracker
Monarch Mapping Commons SSSOM Mappings collected and curated by the Monarch Initiative. Issue Tracker
HPO Language Translations Infrastructure to collect and coordinate HPO language translations. Issue Tracker
Phenomizer A web application for clinical diagnostics in human genetics using semantic similarity searches in ontologies. Issue Tracker
Phenogrid Phenogrid is a web component that visualizes semantic similarity calculations provided by OWLSim, as provided through APIs from the Monarch Initiative. Issue Tracker
Monarch Assistant An LLM retrieval augmented generation (RAG) agent for Monarch Initiative. Issue Tracker

Data documentation

Repository Description Tracker
HPOA - Disease Annotations Issue Tracker
HPOA - Phenotype to Gene Associations Issue Tracker
HPOA - Gene to Phenotype Associations Issue Tracker
HPOA Knowledge Graph Ingestible Issue Tracker
Alliance Knowledge Graph Ingestible Issue Tracker

Other documentation and training materials

Repository Description Tracker
OBO Academy A resource for self-paced training of Semantic Engineers. Issue Tracker
Best practices for collaborative open source coding The best practice / house style guide maintained by Monarch's LBNL team members. Issue Tracker